Boogiepop Phantom - Just trying to trace all the cross-connections through the series can induce acid flashbacks.
Pani Poni Dash - Already mentioned, but worth mentioning again.
FLCL - of course
Dai Mahou Touge - If you haven't seen this, you've missed something truly bizarre.
And, I think I'll throw "Best Student Council" in for good measure. There is something truly twisted at the heart of that anime.